Early life microbial succession in the gut follows common patterns in humans across the globe

Guilherme Fahur Bottino, Kevin S. Bonham, Fadheela Patel, Shelley McCann, Michal Zieff, Nathalia Naspolini, Daniel Ho, Theo Portlock, Raphaela Joos, Firas S. Midani, Paulo Schüroff, Anubhav Das, Inoli Shennon, Brooke C. Wilson, Justin M. O’Sullivan, Robert A. Britton, Deirdre M. Murray, Mairead E. Kiely, Carla R. Taddei, Patrícia C. B. Beltrão-Braga, Alline C. Campos, Guilherme V. Polanczyk, Curtis Huttenhower, Kirsten A. Donald and Vanja Klepac-Ceraj ()
Additional contact information
Guilherme Fahur Bottino: Wellesley College
Kevin S. Bonham: Wellesley College
Fadheela Patel: University of Cape Town
Shelley McCann: Wellesley College
Michal Zieff: University of Cape Town
Nathalia Naspolini: University of São Paulo
Daniel Ho: The University of Auckland
Theo Portlock: The University of Auckland
Raphaela Joos: APC Microbiome Ireland
Firas S. Midani: Baylor College of Medicine
Paulo Schüroff: University of São Paulo
Anubhav Das: APC Microbiome Ireland
Inoli Shennon: The University of Auckland
Brooke C. Wilson: The University of Auckland
Justin M. O’Sullivan: The University of Auckland
Robert A. Britton: Baylor College of Medicine
Deirdre M. Murray: University College Cork
Mairead E. Kiely: University College Cork
Carla R. Taddei: University of São Paulo
Patrícia C. B. Beltrão-Braga: University of São Paulo
Alline C. Campos: Ribeirão Preto Medical School- University of São Paulo
Guilherme V. Polanczyk: Universidade de São Paulo
Curtis Huttenhower: Harvard T.H. Chan School of Public Health
Kirsten A. Donald: University of Cape Town
Vanja Klepac-Ceraj: Wellesley College

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of “microbiome age” for assessing early gut maturation that may be used alongside other measures of child development.

Date: 2025
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DOI: 10.1038/s41467-025-56072-w

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